FirstGlance/Visualizing Conservation: Difference between revisions
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===Optimization=== | ===Optimization=== | ||
Before going further, it is good to decide whether the results are satisfactory, or need optimization. Lets consider [[7bak]], a drug-target protease of SARS-CoV-2 (see [https://pdb101.rcsb.org/motm/242 Coronavirus Proteases]). A ConSurf run with all default settings left 10% of the residues with insufficient data<ref name="insufficientdata">When the confidence interval for a conservation value of an amino acid is too large, ConSurf reports "insufficient data" (uncertainty: yellow color). See [https://consurf.tau.ac.il/quick_help.php#RELIABILITY Position Specific Quality] and [https://consurf.tau.ac.il/overview.php#_Toc311131298 Confidence Interval] in the ConSurf documentation.</ref> (yellow color), and the diversity in the multiple sequence alignment (MSA) was too low ([[Interpreting_ConSurf_Results#Average_Pairwise_Distance|average pairwise distance]] 0.34), leaving conservation grades 2 and 3 almost unoccupied. These inadequacies are highlighted by a distribution report displayed by FirstGlance. | Before going further, it is good to decide whether the results are satisfactory, or need optimization. Lets consider [[7bak]], a drug-target protease of SARS-CoV-2 (see [https://pdb101.rcsb.org/motm/242 Coronavirus Proteases]). | ||
:[https://www.bioinformatics.org/firstglance/fgij3.8beta2/fg.htm?mol=7bak_consurf1641000454_pipe.pdb Display 7BAK ConSurf Result in FirstGlance 3.8Beta2] | |||
A ConSurf run with all default settings left 10% of the residues with insufficient data<ref name="insufficientdata">When the confidence interval for a conservation value of an amino acid is too large, ConSurf reports "insufficient data" (uncertainty: yellow color). See [https://consurf.tau.ac.il/quick_help.php#RELIABILITY Position Specific Quality] and [https://consurf.tau.ac.il/overview.php#_Toc311131298 Confidence Interval] in the ConSurf documentation.</ref> (yellow color), and the diversity in the multiple sequence alignment (MSA) was too low ([[Interpreting_ConSurf_Results#Average_Pairwise_Distance|average pairwise distance]] 0.34), leaving conservation grades 2 and 3 almost unoccupied. These inadequacies are highlighted by a distribution report displayed by FirstGlance. | |||
<br> | <br> | ||
[[Image:7bak-consurf-dist-defaults.png]] | [[Image:7bak-consurf-dist-defaults.png]] | ||
